Esquire made big news in the world of paid Web content in July, putting one of its magazine features behind a paywall. “The Prophet”—for sale on Esquire.com for $1.99—wasn’t the title’s first experience with a paywall though.

To avoid trolls and curb distracting dialogues, some publishers have given up on commenting by removing the option all together or burying the section at the bottom of the page. Others, however, are confronting the challenge head on and finding...